So Seattle’s newcomers and longtime residents alike may wonder: Is it actually safe to swim in Green Lake? And what about Lake Washington and Lake Union?

Despite its reputation, Green Lake is clean and safe for swimmers, according to routine testing by King County. The same goes for Lake Washington. In Lake Union, it’s actually illegal to swim, in part because of busy boat traffic.

Green Lake beaches, scientists say, often have lower bacteria levels than the beaches of Lake Washington, its seemingly fresher and larger aquatic counterpart.

“People aren’t used to the new ‘clean green,’ ” said Rob Zisette, president of Friends of Green Lake. “People ask, ‘How could it not be polluted? It’s in the middle of an urban area, so how could it not?’ But that’s not the case.”

Zisette is also a limnologist — limnology is the study of inland waters — so he knows Green Lake well, and how it compares with other Seattle-area lakes. He says the lake’s water quality is now in great condition. Two years ago, the water was treated with nontoxic alum, which reduces the level of phosphorous that promotes toxic algae growth.

It wasn’t always this way. Before a more concerted cleanup effort began in the early 2000s, the lake was, as Zisette describes it, a cesspool.

“It smelled,” he said. “It got so bad that it was kind of nauseating to even walk around it.”

Swimmers complained of welts on their skin after leaving the water, a more severe form of “swimmers itch” that earned a more specific name: “Green Lake itch.” But water treatments helped, and swimmers itch — a rash caused from an allergic reaction to certain parasites — isn’t as common.

Seattle Parks and Recreation says swimmers should take a soap shower immediately after swimming to avoid itchiness. Rinsing off with any water is the second best option, but if there’s no shower available, it’s better to dry off with a towel instead of air drying.

Don’t swallow the water. Along with toxic algae, another health concern is fecal contamination, which is more likely in Lake Washington than Green Lake, because there’s no sewage input in Green Lake. An area with more than 1,000 colony-forming units (CFUs) of fecal bacteria per 100 milliliters of water is considered unsafe for swimming, according to the King County Swimming Beaches Program. A sample from west Green Lake beach, for example, measured 3 CFUs per 100 mL of water last week.

“We can tell you what it was like at the time we collected a sample, but we can’t tell you what happened three hours later, when someone was sick and had a ‘fecal incident,’ ” said Debra Bouchard, a King County senior limnologist and water-quality planner.

The middle of a lake has less bacteria than at beaches, but swimmers must stay in designated swim areas and within 50 feet of shore, according to the City of Seattle. Boaters can take a dip, but they shouldn’t swim beyond 25 feet of the boat. The boat must have a life jacket for all people swimming in the water.

Swimming isn’t allowed in Lake Union at all, because of boat traffic on the lake. If law-enforcement officers see someone swimming in the lake, they usually tell them to get out without citing them, Seattle Police Department spokesman Mark Jamieson said.

Overall, the limnologists say, trust your own best judgment. Swimming in an off-leash area for dogs, for example, might not be advisable, because there’s a potential for an increase in bacteria.